// Copyright (C) The Arvados Authors. All rights reserved. // // SPDX-License-Identifier: AGPL-3.0 package crunchrun import ( "bytes" "fmt" "io" "io/ioutil" "os" "os/exec" "strings" "git.arvados.org/arvados.git/sdk/go/arvados" "git.arvados.org/arvados.git/sdk/go/arvadosclient" "git.arvados.org/arvados.git/sdk/go/arvadostest" "git.arvados.org/arvados.git/sdk/go/keepclient" . "gopkg.in/check.v1" ) var _ = Suite(&integrationSuite{}) type integrationSuite struct { engine string image arvados.Collection input arvados.Collection stdin bytes.Buffer stdout bytes.Buffer stderr bytes.Buffer cr arvados.ContainerRequest client *arvados.Client ac *arvadosclient.ArvadosClient kc *keepclient.KeepClient } func (s *integrationSuite) SetUpSuite(c *C) { _, err := exec.LookPath("docker") if err != nil { c.Skip("looks like docker is not installed") } arvadostest.StartKeep(2, true) out, err := exec.Command("docker", "load", "--input", busyboxDockerImage(c)).CombinedOutput() c.Log(string(out)) c.Assert(err, IsNil) out, err = exec.Command("arv-keepdocker", "--no-resume", "busybox:uclibc").Output() imageUUID := strings.TrimSpace(string(out)) c.Logf("image uuid %s", imageUUID) c.Assert(err, IsNil) err = arvados.NewClientFromEnv().RequestAndDecode(&s.image, "GET", "arvados/v1/collections/"+imageUUID, nil, nil) c.Assert(err, IsNil) c.Logf("image pdh %s", s.image.PortableDataHash) s.client = arvados.NewClientFromEnv() s.ac, err = arvadosclient.New(s.client) c.Assert(err, IsNil) s.kc = keepclient.New(s.ac) fs, err := s.input.FileSystem(s.client, s.kc) c.Assert(err, IsNil) f, err := fs.OpenFile("inputfile", os.O_CREATE|os.O_WRONLY, 0755) c.Assert(err, IsNil) _, err = f.Write([]byte("inputdata")) c.Assert(err, IsNil) err = f.Close() c.Assert(err, IsNil) s.input.ManifestText, err = fs.MarshalManifest(".") c.Assert(err, IsNil) err = s.client.RequestAndDecode(&s.input, "POST", "arvados/v1/collections", nil, map[string]interface{}{ "ensure_unique_name": true, "collection": map[string]interface{}{ "manifest_text": s.input.ManifestText, }, }) c.Assert(err, IsNil) c.Logf("input pdh %s", s.input.PortableDataHash) } func (s *integrationSuite) TearDownSuite(c *C) { if s.client == nil { // didn't set up return } err := s.client.RequestAndDecode(nil, "POST", "database/reset", nil, nil) c.Check(err, IsNil) } func (s *integrationSuite) SetUpTest(c *C) { s.engine = "docker" s.stdin = bytes.Buffer{} s.stdout = bytes.Buffer{} s.stderr = bytes.Buffer{} s.cr = arvados.ContainerRequest{ Priority: 1, State: "Committed", OutputPath: "/mnt/out", ContainerImage: s.image.PortableDataHash, Mounts: map[string]arvados.Mount{ "/mnt/json": { Kind: "json", Content: []interface{}{ "foo", map[string]string{"foo": "bar"}, nil, }, }, "/mnt/in": { Kind: "collection", PortableDataHash: s.input.PortableDataHash, }, "/mnt/out": { Kind: "tmp", Capacity: 1000, }, }, RuntimeConstraints: arvados.RuntimeConstraints{ RAM: 128000000, VCPUs: 1, API: true, }, } } func (s *integrationSuite) setup(c *C) { err := s.client.RequestAndDecode(&s.cr, "POST", "arvados/v1/container_requests", nil, map[string]interface{}{"container_request": map[string]interface{}{ "priority": s.cr.Priority, "state": s.cr.State, "command": s.cr.Command, "output_path": s.cr.OutputPath, "container_image": s.cr.ContainerImage, "mounts": s.cr.Mounts, "runtime_constraints": s.cr.RuntimeConstraints, "use_existing": false, }}) c.Assert(err, IsNil) c.Assert(s.cr.ContainerUUID, Not(Equals), "") err = s.client.RequestAndDecode(nil, "POST", "arvados/v1/containers/"+s.cr.ContainerUUID+"/lock", nil, nil) c.Assert(err, IsNil) } func (s *integrationSuite) TestRunTrivialContainerWithDocker(c *C) { s.engine = "docker" s.testRunTrivialContainer(c) } func (s *integrationSuite) TestRunTrivialContainerWithSingularity(c *C) { s.engine = "singularity" s.testRunTrivialContainer(c) } func (s *integrationSuite) testRunTrivialContainer(c *C) { if err := exec.Command("which", s.engine).Run(); err != nil { c.Skip(fmt.Sprintf("%s: %s", s.engine, err)) } s.cr.Command = []string{"sh", "-c", "cat /mnt/in/inputfile >/mnt/out/inputfile && cat /mnt/json >/mnt/out/json && ! touch /mnt/in/shouldbereadonly && mkdir /mnt/out/emptydir"} s.setup(c) code := command{}.RunCommand("crunch-run", []string{ "-runtime-engine=" + s.engine, "-enable-memory-limit=false", s.cr.ContainerUUID, }, &s.stdin, io.MultiWriter(&s.stdout, os.Stderr), io.MultiWriter(&s.stderr, os.Stderr)) c.Check(code, Equals, 0) err := s.client.RequestAndDecode(&s.cr, "GET", "arvados/v1/container_requests/"+s.cr.UUID, nil, nil) c.Assert(err, IsNil) c.Logf("Finished container request: %#v", s.cr) var log arvados.Collection err = s.client.RequestAndDecode(&log, "GET", "arvados/v1/collections/"+s.cr.LogUUID, nil, nil) c.Assert(err, IsNil) fs, err := log.FileSystem(s.client, s.kc) c.Assert(err, IsNil) if d, err := fs.Open("/"); c.Check(err, IsNil) { fis, err := d.Readdir(-1) c.Assert(err, IsNil) for _, fi := range fis { if fi.IsDir() { continue } f, err := fs.Open(fi.Name()) c.Assert(err, IsNil) buf, err := ioutil.ReadAll(f) c.Assert(err, IsNil) c.Logf("\n===== %s =====\n%s", fi.Name(), buf) } } var output arvados.Collection err = s.client.RequestAndDecode(&output, "GET", "arvados/v1/collections/"+s.cr.OutputUUID, nil, nil) c.Assert(err, IsNil) fs, err = output.FileSystem(s.client, s.kc) c.Assert(err, IsNil) if f, err := fs.Open("inputfile"); c.Check(err, IsNil) { defer f.Close() buf, err := ioutil.ReadAll(f) c.Check(err, IsNil) c.Check(string(buf), Equals, "inputdata") } if f, err := fs.Open("json"); c.Check(err, IsNil) { defer f.Close() buf, err := ioutil.ReadAll(f) c.Check(err, IsNil) c.Check(string(buf), Equals, `["foo",{"foo":"bar"},null]`) } if fi, err := fs.Stat("emptydir"); c.Check(err, IsNil) { c.Check(fi.IsDir(), Equals, true) } if d, err := fs.Open("emptydir"); c.Check(err, IsNil) { defer d.Close() fis, err := d.Readdir(-1) c.Assert(err, IsNil) // crunch-run still saves a ".keep" file to preserve // empty dirs even though that shouldn't be // necessary. Ideally we would do: // c.Check(fis, HasLen, 0) for _, fi := range fis { c.Check(fi.Name(), Equals, ".keep") } } }